Yeah I really don't understand the thinking with the audio commentary. It's free to download so why not just put it on the disc? Makes no sense.

It's more than just a separate audio track - it's a separate cut of the film (no additional movie footage) with additional on-screen annotations and a bunch of other stuff built in as well.

That could still easily be included with the disc, and would probably even be better suited for the BR format, where it can be an optional (interactive?) overlay track, rather than hard-coded onto the video itself. It also would require a drastic amount of space on the disc itself.